The coastal areas of the southern Red Sea islands are non-urbanized, relatively pristine environments and are located on the main migration pathway of Indo-Pacific foraminiferal species to the northern Red Sea and to the Mediterranean Sea via the Suez Canal. Studying the foraminiferal composition, structure, and distribution in the Red Sea is essential to understanding how Indo-Pacific species can migrate to and survive in the Mediterranean Sea. Al-Bawadi, an uninhabited island located in the southern Red Sea, is an ideal location for such study. The coastal waters are oligotrophic, hypersaline, and very warm, overlying carbonate-rich, sandy-bottom and coral-reef substrata. In 25 sediment samples collected from water depths <6 m, 79 foraminiferal species were recorded. Rotaliids dominated the assemblages, followed by miliolids; agglutinated foraminifers were scarce, and planktic species were not found. The larger-benthic, symbiont-bearing Neorotalia calcar dominated except in very shallow water, where smaller, free-living miliolid species dominated. The FoRAM Index (FI) was calculated for all samples; the symbiont-bearing group included seven genera comprising more than half of the total assemblage such that the FI>4 for most samples from depths >3 m, indicating that water quality is suitable for coral-reef growth and recovery. Diversity indices reflected prevailing normal marine to hypersaline conditions. Depth, presence of coral reefs, and hydrodynamics are the main factors controlling the spatial distribution of the foraminiferal assemblages. Occurrences of aberrant tests in the tidal flat area could be related to naturally occurring stresses, such as rapid changes in temperature and salinity, or to breakage and repair. Monitoring studies of unthreatened environments are essential to understand reef-related assemblages and to predict the migration pathways of thermo-tolerant and thermo-sensitive foraminiferal species.